Bacterial selection in the rhizosphere soils of different rice genotypes with yield variance

Improving the use efficiency of nitrogen by rice crop has been receiving much attention in recent years due to overuse of nitrogen fertilizer that has caused series of environmental problems. Different genotypes of rice plants could select specific rhizospheric microbial populations responsible for elemental cycles. However, how the functional bacteria in the rhizosphere regulate rice genotypes varying in nitrogen use efficiency remain unknown. We calculated the nitrogen utilization efficiencies of different rice genotypes and applied 16S ribosomal RNA gene sequencing to characterize the functional rhizosphere bacteria of the rice genotypes with yield variance. Our results revealed that rice genotypes selected their specific microbial communities inhabiting the rhizosphere, shaping the rhizospheric bacteria both at the taxonomic and functional levels. The bacterial groups were mainly involved in the functions of metal-ion reduction, nitrogen transformation, and organic compound biodegradation. The rhizosphere functional bacterial communities were closely correlated with the yield, especially the groups of Proteobacteria and Chloroflexi at the phylum level. Further investigation of the nitrogen-cycling genes by real-time PCR showed that the productive genotypes had low abundances of denitrifying genes in the rhizosphere, revealing less nitrogen loss but higher available nitrogen supply to the rice genotypes. This investigation helps to reveal how functional bacteria assembled in the rhizosphere of rice genotypes with varying nitrogen use efficiencies, providing valuable information with regard to the reduction of fertilizer application through the selection of rice genotypes.